If I use any commercial or free/opensource/ CMS's CSS and JavaScript with existing CSS classes, IDs and variable names can it be a copyright issue?
It shouldn't be much of issue for free/opensource, however, if there is commercial one, then it could be an issue. The point is that you should go and see there license type and see what is permitted according to that license .
It could also potentially be a patent violation, although I would think that the legal workings became murkier. Apart from serious code, I think it is conceivable that someone somewhere might attempt to define certain Javascript functionality as part of the application logic. CSS is harder.
It is also relevant to your question what could be pursued in court as a copyright violation, as content that is copyrighted and then plagiarised doesn't necessarily make it something that can be defended in court.
Only a lawyer in a relevant jurisdiction could properly answer your question, and my guess is that you would get slightly different opinions/interpretations on a specific case from different lawyers.